Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/51f0dd69a74773e008792cb7841328/fi_workdir/659_cRB-T1-TRNA-1_B23WHTKLT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/27769222abc8540e2b3fe9aca3b438/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/27769222abc8540e2b3fe9aca3b438/.command.run
==> STAGING COMPLETE (3 inputs)
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/agat_config.yaml file
------------------------------------------------------------------------------
| Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0 |
| https://github.com/NBISweden/AGAT |
| National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se |
------------------------------------------------------------------------------
------ Start parsing ------
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
* locus_tag
* gene_id
=> merge_loci option deactivated
=> Machine information:
This script is being run by perl v5.32.1
Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
Operating system being used: linux
=> Accessing Ontology
No ontology accessible from the gff file header!
We use the SOFA ontology distributed with AGAT:
/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
4 root terms, and 2596 total terms, and 1516 leaf terms
Filtering ontology:
We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 847
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 847
=> Number of feature type (3rd column): 2
* Level1: 0 =>
* level2: 0 =>
* level3: 2 => exon CDS
* unknown: 0 =>
=>Check because only level3 features:
* Number of feature with Parent attribute:0
* Number of feature with a common attribute:847
=> Some common attributes and some Parent attributes missing.
/!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
/!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
!! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
------ End parsing (done in 0 second) ------
------ Start checks ------
---------------------------- Check1: feature types -----------------------------
----------------------------------- ontology -----------------------------------
All feature types in agreement with the Ontology.
------------------------------------- agat -------------------------------------
AGAT can deal with all the encountered feature types (3rd column)
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check2: duplicates ------------------------------
None found
------------------------------ done in 0 seconds -------------------------------
-------------------------- Check3: sequential bucket ---------------------------
Nothing to check as sequential bucket!
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created:
PTPRK--RSPO3 HAVANA gene 53093 62586 . + . FI_gene_label "RSPO3^ENSG00000146374.14" ; ID "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; ccdsid "CCDS5135.1" ; exon_id "ENSE00001858691.2" ; exon_number 1 ; gene_id "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; gene_name RSPO3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015521.2" ; havana_transcript "OTTHUMT00000042111.2" ; hgnc_id "HGNC:20866" ; level 2 ; orig_coord_info "chr6,127119193,127119289,+" ; protein_id "ENSP00000349131.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PTPRK--RSPO3^ENST00000356698.9" ; transcript_name "RSPO3-201" ; transcript_support_level 1 ; transcript_type protein_coding
PTPRK--RSPO3 HAVANA mRNA 53093 62586 . + . FI_gene_label "RSPO3^ENSG00000146374.14" ; ID "PTPRK--RSPO3^ENST00000356698.9" ; Parent "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; ccdsid "CCDS5135.1" ; exon_id "ENSE00001858691.2" ; exon_number 1 ; gene_id "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; gene_name RSPO3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015521.2" ; havana_transcript "OTTHUMT00000042111.2" ; hgnc_id "HGNC:20866" ; level 2 ; orig_coord_info "chr6,127119193,127119289,+" ; protein_id "ENSP00000349131.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PTPRK--RSPO3^ENST00000356698.9" ; transcript_name "RSPO3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PTPRK--RSPO3 HAVANA gene 1034 48764 . + . FI_gene_label "PTPRK^ENSG00000152894.15" ; ID "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; exon_id "ENSE00002151979.1" ; exon_number 1 ; gene_id "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; gene_name PTPRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000015536.10" ; havana_transcript "OTTHUMT00000390045.1" ; hgnc_id "HGNC:9674" ; level 2 ; orig_coord_info "chr6,128520259,128520358,-" ; protein_id "ENSP00000357190.3" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "PTPRK--RSPO3^ENST00000368207.7" ; transcript_name "PTPRK-203" ; transcript_support_level 5 ; transcript_type protein_coding
PTPRK--RSPO3 HAVANA mRNA 1034 48764 . + . FI_gene_label "PTPRK^ENSG00000152894.15" ; ID "PTPRK--RSPO3^ENST00000368207.7" ; Parent "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; exon_id "ENSE00002151979.1" ; exon_number 1 ; gene_id "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; gene_name PTPRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000015536.10" ; havana_transcript "OTTHUMT00000390045.1" ; hgnc_id "HGNC:9674" ; level 2 ; orig_coord_info "chr6,128520259,128520358,-" ; protein_id "ENSP00000357190.3" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "PTPRK--RSPO3^ENST00000368207.7" ; transcript_name "PTPRK-203" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC025884.2--IGH-@-ext HAVANA gene 1001 1711 . + . FI_gene_label "AC025884.2^ENSG00000259098.1" ; ID "AC025884.2--IGH-@-ext^AC025884.2^ENSG00000259098.1" ; exon_id "ENSE00002441536.1" ; exon_number 1 ; gene_id "AC025884.2--IGH-@-ext^AC025884.2^ENSG00000259098.1" ; gene_name "AC025884.2" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000171790.1" ; havana_transcript "OTTHUMT00000415152.1" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr15,22258138,22258848,+" ; tag basic ; transcript_id "AC025884.2--IGH-@-ext^ENST00000553429.1" ; transcript_name "AC025884.2-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
AC025884.2--IGH-@-ext HAVANA RNA 1001 1711 . + . FI_gene_label "AC025884.2^ENSG00000259098.1" ; ID "AC025884.2--IGH-@-ext^ENST00000553429.1" ; Parent "AC025884.2--IGH-@-ext^AC025884.2^ENSG00000259098.1" ; exon_id "ENSE00002441536.1" ; exon_number 1 ; gene_id "AC025884.2--IGH-@-ext^AC025884.2^ENSG00000259098.1" ; gene_name "AC025884.2" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000171790.1" ; havana_transcript "OTTHUMT00000415152.1" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr15,22258138,22258848,+" ; tag basic ; transcript_id "AC025884.2--IGH-@-ext^ENST00000553429.1" ; transcript_name "AC025884.2-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
AC025884.2--IGH-@-ext SuperLocus-ext gene 4712 1296052 . + . FI_gene_label "IGH-@-ext^IGH-.g@-ext" ; ID "AC025884.2--IGH-@-ext^IGH-@-ext^IGH-.g@-ext" ; gene_id "AC025884.2--IGH-@-ext^IGH-@-ext^IGH-.g@-ext" ; gene_name "IGH-@-ext" ; orig_coord_info "chr14,105583731,106875071,+" ; transcript_id "AC025884.2--IGH-@-ext^IGH-.t@-ext"
AC025884.2--IGH-@-ext SuperLocus-ext RNA 4712 1296052 . + . FI_gene_label "IGH-@-ext^IGH-.g@-ext" ; ID "AC025884.2--IGH-@-ext^IGH-.t@-ext" ; Parent "AC025884.2--IGH-@-ext^IGH-@-ext^IGH-.g@-ext" ; gene_id "AC025884.2--IGH-@-ext^IGH-@-ext^IGH-.g@-ext" ; gene_name "IGH-@-ext" ; orig_coord_info "chr14,105583731,106875071,+" ; transcript_id "AC025884.2--IGH-@-ext^IGH-.t@-ext"
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1 HAVANA RNA 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^ENST00000624936.2" ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
46 cases fixed where L3 features have parent feature(s) missing
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
------------------------------ done in 0 seconds -------------------------------
------------------------- Check7: all level3 locations -------------------------
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check8: check cds -------------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check10: check utrs ------------------------------
80 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 0 seconds -------------------------------
------------------------ Check11: all level2 locations -------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
------------------------ Check12: all level1 locations -------------------------
We fixed 2 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------
---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
------ End checks (done in 0 second) ------
GFF3 file parsed